def drawMatrix(data):
panel = markup.page()
helper.link_css_and_js(panel)
full_names = {'dom': 'Domesticus', 'mus': 'Musculus', 'cas': 'Castaneus', 'unk': 'Unknown'}
panel.table()
panel.tr()
panel.td('')
panel.td("Distal interval: Chromosome {}: {:,} - {:,}".format(*tuple(data['Intervals'][1])))
panel.tr.close()
panel.tr()
panel.td("Proximal interval: Chromosome {}: {:,} - {:,}".format(*tuple(data['Intervals'][0])))
panel.td()
panel.table(_class="table table-striped")
panel.tr()
panel.th('')
for subspecies in data['Key']:
panel.th(full_names[subspecies])
panel.tr.close()
for subspecies, samples in zip(data['Key'], data['Samples']):
panel.tr()
panel.th(full_names[subspecies])
for sample_set in samples:
panel.td(', '.join(sample_set) or '-')
panel.tr.close()
panel.table.close()
panel.td.close()
panel.tr.close()
panel.table.close()
return panel
def indexPage(form):
tl = twolocus.TwoLocus("/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/")
panel = markup.page()
helper.link_css_and_js(panel)
panel.div(style="padding:20px 20px;")
user, permissionLevel, date, time, elapsed = cgAdmin.getCompgenCookie(form)
editFlag = form.getvalue("edit") == "True"
if permissionLevel >= 80:
panel.add(WikiApp.editTag("%s" % this_file, not editFlag))
panel.add(
WikiApp.getWikiContent(
"%s" % this_file, editInPlace=(permissionLevel >= 80) and editFlag, returnPage="./?run=%s" % this_file
)
)
panel.br()
panel.form(_class="form-horizontal", action="", method="POST", enctype="multipart/form-data")
panel.div(_class="control-group")
panel.h3("Set of Samples")
has_strains = helper.strain_set_selector(panel, tl)
panel.script(type="text/javascript")
panel.add("""$(".chosen").chosen()""")
panel.script.close()
helper.select_all_buttons(panel)
panel.br()
panel.input(type="hidden", name="target", value="%s.originsVisualization" % this_file)
panel.input(type="submit", name="submit", value="Submit")
panel.div.close() # control group
panel.form.close()
panel.div.close()
panel.script("""$("form").submit(function(event) {return %s(event);});""" % has_strains, type="text/javascript")
return panel
def uniqueCombosResponse(form):
# print "content-type: text/json\n"
tl = twolocus.TwoLocus("/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/")
strains = [[], []]
for set_num, set_id in enumerate(["background", "foreground"]):
for _, _, value, _ in helper.STRAIN_SETS:
new_strains = form.getvalue(value + set_id)
if type(new_strains) is list:
strains[set_num] += new_strains
elif new_strains is not None:
strains[set_num].append(new_strains)
# print '\n'.join(hex(line[0]) + ' ' + ' '.join(map(str, line[1:])) for line in tl.unique_combos(strains[0], strains[1]))
data = json.dumps(tl.unique_combos(strains[0], strains[1]), cls=helper.NumpyEncoder)
# with open('unique.json', "w+") as fp:
# with open('unique.json', "r") as fp:
# json.dump(tl.unique_combos(strains[0], strains[1]), fp, cls=helper.NumpyEncoder)
# data = json.load(fp)
# data = '0'
# panel = markup.page()
# panel.iframe(src='../sgreens/pairwise_origins/pairwiseGenome.html', chartWidth="100%", chartHeight="1000px")
# return panel
# print "content-type: text/html\n"
# with open('../sgreens/pairwise_origins/pairwiseGenome.html') as fp:
# print fp.read()<!DOCTYPE html>
helper.visualize_genome(data, tl)
def indexPage(form):
tl = twolocus.TwoLocus('/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/')
panel = markup.page()
helper.link_css_and_js(panel)
panel.div(style="padding:20px 20px;")
user, permissionLevel, date, time, elapsed = cgAdmin.getCompgenCookie(form)
editFlag = (form.getvalue("edit") == "True")
if permissionLevel >= 80:
panel.add(WikiApp.editTag("%s" % this_file, not editFlag))
panel.add(WikiApp.getWikiContent("%s" % this_file, editInPlace=(permissionLevel >= 80) and editFlag,
returnPage="./?run=%s" % this_file))
panel.br()
panel.form(_class="form-horizontal", action="", method="POST", enctype="multipart/form-data")
panel.div(_class="control-group")
panel.h3('Set of Samples')
has_strains = helper.strain_set_selector(panel, tl)
for pos_num in ('1', '2'):
panel.h3('Position ' + pos_num)
helper.open_control(panel, 'Chromosome')
panel.select(_class="medium", name="chrom" + pos_num)
for chrom_num in xrange(1, 19):
panel.option(chrom_num)
panel.option('X', value='X')
panel.select.close()
helper.close_control(panel)
helper.open_control(panel, 'Position')
panel.add('''<input class="input-medium" name="pos%s" required pattern="\d+[\d,]*\.?\d*[mMkK]*">'''
% pos_num)
panel.add("""<p class="help-block">3000000 = 3,000,000 = 3m = 3M = 3000k = 3KK</p>""")
helper.close_control(panel)
panel.script(type="text/javascript")
panel.add("""$(".chosen").chosen()""")
panel.script.close()
helper.select_all_buttons(panel)
panel.br()
panel.input(type="hidden", name="target", value="%s.countMatrix" % this_file)
panel.input(type="submit", name="submit", value="Submit")
panel.div.close() # control group
panel.form.close()
panel.div.close()
chromo_sizes = {}
for string, integer in twolocus.CHROMO_TO_INT.iteritems():
chromo_sizes[string] = tl.sizes[integer-1]
panel.script('''
var chromoSizes = %s;
''' % json.dumps(chromo_sizes), type="text/javascript")
panel.script('''
function parsePosition(string) {
string = string.replace(',','').toLowerCase();
var pos = parseFloat(string);
var units = '';
var char
for (var i = 0; i < string.length; i++) {
char = string[i];
if (char == 'm' || char == 'k') {
pos = parseFloat(string.substring(0, i));
units = string.substring(i);
break;
}
}
for (i = 0; i < units.length; i++) {
char = units[i];
if (char == 'k') {
pos *= 1000;
}
if (char == 'm') {
pos *= 1000000;
}
}
return Math.floor(pos);
}
function isValidIndex(chromosome, position) {
return (chromosome in chromoSizes) && (0 <= position) && (position <= chromoSizes[chromosome]);
}
$("form").submit(function(event) {
var chrom, pos;
isValidInput = true;
for (var i = 1; i <= 2; i++) {
chrom = document.getElementsByName('chrom' + i)[0].value;
pos = parsePosition(document.getElementsByName('pos' + i)[0].value);
if (!isValidIndex(chrom, pos)) {
alert("Position " + i + " exceeds chromosome length");
isValidInput = false;
}
}
return %s(event) && isValidInput;
});
''' % has_strains, type="text/javascript")
return panel
def originsVisualizationResponse(form):
# print "content-type: text/json\n"
coarse_cutoff = 1e7
panel = markup.page()
plot_file = "ss_origins.html"
bokeh.plotting.output_file(plot_file)
tl = twolocus.TwoLocus("/csbiodata/public/www.csbio.unc.edu/htdocs/sgreens/pairwise_origins/")
strains = []
for _, _, value, _ in helper.STRAIN_SETS:
new_strains = form.getvalue(value)
if type(new_strains) is list:
strains += new_strains
elif new_strains is not None:
strains.append(new_strains)
data, colors = tl.pairwise_frequencies(strains)
absent_regions = tl.absent_regions(strains)
plot = bokeh.plotting.figure(
y_range=bokeh.models.Range1d(start=tl.offsets[-1] + 10e7, end=0),
height=750,
width=750,
background_fill_color="black",
tools=[
"tap",
"resize",
bokeh.models.HoverTool(names=["chroms"], tooltips=[("Proximal", "@proximal"), ("Distal", "@distal")]),
],
)
plot.axis.visible = False
plot.grid.grid_line_color = None
for combo_regions, color in zip(data, colors):
region_widths = np.subtract(combo_regions[1], combo_regions[0])
region_heights = np.subtract(combo_regions[3], combo_regions[2])
coarse_indices = np.logical_or(region_widths > coarse_cutoff, region_heights > coarse_cutoff)
region_widths = region_widths[coarse_indices]
region_heights = region_heights[coarse_indices]
x_positions = np.add(np.array(combo_regions[0])[coarse_indices], region_widths / 2)
y_positions = np.add(np.array(combo_regions[2])[coarse_indices], region_heights / 2)
plot.rect(
x_positions,
y_positions,
region_widths,
region_heights,
color="#" + hex(color)[2:].zfill(6),
fill_alpha=1.0 / len(strains),
line_alpha=0,
)
break
for combo_regions in absent_regions:
region_widths = np.subtract(combo_regions[1], combo_regions[0])
region_heights = np.subtract(combo_regions[3], combo_regions[2])
coarse_indices = np.logical_or(region_widths > coarse_cutoff, region_heights > coarse_cutoff)
region_widths = region_widths[coarse_indices]
region_heights = region_heights[coarse_indices]
x_positions = np.add(np.array(combo_regions[0])[coarse_indices], region_widths / 2)
y_positions = np.add(np.array(combo_regions[2])[coarse_indices], region_heights / 2)
plot.rect(x_positions, y_positions, region_widths, region_heights, color="white")
break
chrom_data = dict(x=[], y=[], width=[], height=[], proximal=[], distal=[])
for i in xrange(len(tl.sizes)):
for j in xrange(i, len(tl.sizes)):
chrom_data["x"].append(tl.offsets[i] + tl.sizes[i] / 2)
chrom_data["y"].append(tl.offsets[j] + tl.sizes[j] / 2)
chrom_data["width"].append(tl.sizes[i])
chrom_data["height"].append(tl.sizes[j])
chrom_data["proximal"].append(twolocus.INT_TO_CHROMO[i + 1])
chrom_data["distal"].append(twolocus.INT_TO_CHROMO[j + 1])
chrom_data_source = bokeh.models.ColumnDataSource(data=chrom_data)
plot.rect(
x="x",
y="y",
width="width",
height="height",
fill_alpha=0,
line_color="grey",
hover_alpha=0.5,
name="chroms",
source=chrom_data_source,
)
text_offsets = tl.offsets.copy()[:-1]
text_offsets[-3] += 5e7
plot.text(
x=-15e7,
y=[offset + 10e7 for offset in text_offsets],
text=twolocus.INT_TO_CHROMO[1:],
text_color="white",
text_font_size="10pt",
)
plot.text(
x=text_offsets,
y=tl.offsets[-1] + 10e7,
text=twolocus.INT_TO_CHROMO[1:],
text_color="white",
text_font_size="8pt",
)
inset_plot = bokeh.plotting.figure()
inset_plot.x_range.bounds = "auto"
inset_plot.y_range.bounds = "auto"
inset_data_source = bokeh.models.ColumnDataSource(data=dict(x=[], y=[], width=[], height=[]))
inset_plot.rect("x", "y", "width", "height", color="black")
bokeh.plotting.show(bokeh.io.hplot(plot, inset_plot))
with open(plot_file) as fp:
panel.add(fp.read())
return panel
helper.visualize_genome(data, tl, len(strains))
